I discovered that my monitors configuration are changed by a process called gnome-settings-daemon (one time I found that Filezilla has also changed them ). However, I couldn't find any way to stop this.

What happens is: right now, everything is OK: external monitor is 1600x900 @left, notebook monitor is 1366x768 @right.Sometimes they get both mirrored with 1024x768 resolution.Sometimes they get the right resolutions, but with their positions wrong.